Starting phenix.refine on Sat Dec 28 21:06:32 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6024882.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6024882.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6024882.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.03, per 1000 atoms: 0.60 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 351.6 milliseconds Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 489 0.91 - 1.16: 1142 1.16 - 1.41: 599 1.41 - 1.65: 864 1.65 - 1.90: 59 Bond restraints: 3153 Sorted by residual: bond pdb=" N GLY A 108 " pdb=" CA GLY A 108 " ideal model delta sigma weight residual 1.444 1.641 -0.198 8.80e-03 1.29e+04 5.05e+02 bond pdb=" CA GLY A 108 " pdb=" C GLY A 108 " ideal model delta sigma weight residual 1.511 1.385 0.126 6.90e-03 2.10e+04 3.35e+02 bond pdb=" CA VAL A 35 " pdb=" CB VAL A 35 " ideal model delta sigma weight residual 1.533 1.325 0.208 1.14e-02 7.69e+03 3.33e+02 bond pdb=" N GLY A 174 " pdb=" CA GLY A 174 " ideal model delta sigma weight residual 1.447 1.267 0.179 9.90e-03 1.02e+04 3.28e+02 bond pdb=" C LEU A 7 " pdb=" O LEU A 7 " ideal model delta sigma weight residual 1.236 1.035 0.201 1.14e-02 7.69e+03 3.10e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.69: 3154 4.69 - 9.37: 1888 9.37 - 14.06: 613 14.06 - 18.75: 109 18.75 - 23.44: 13 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 108 " pdb=" C GLY A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 121.07 110.85 10.22 3.60e-01 7.72e+00 8.05e+02 angle pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" O GLY A 74 " ideal model delta sigma weight residual 121.28 137.77 -16.49 1.01e+00 9.80e-01 2.67e+02 angle pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " pdb=" O ACYS A 53 " ideal model delta sigma weight residual 119.71 107.68 12.03 8.10e-01 1.52e+00 2.20e+02 angle pdb=" OD1 ASN A 173 " pdb=" CG ASN A 173 " pdb=" ND2 ASN A 173 " ideal model delta sigma weight residual 122.60 108.37 14.23 1.00e+00 1.00e+00 2.03e+02 angle pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" O ALA A 56 " ideal model delta sigma weight residual 121.10 105.54 15.56 1.10e+00 8.26e-01 2.00e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 21.37: 999 21.37 - 42.72: 84 42.72 - 64.07: 22 64.07 - 85.43: 4 85.43 - 106.78: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -158.63 -21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA VAL A 69 " pdb=" C VAL A 69 " pdb=" N VAL A 70 " pdb=" CA VAL A 70 " ideal model delta harmonic sigma weight residual 180.00 159.22 20.78 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ASP A 49 " pdb=" C ASP A 49 " pdb=" N VAL A 50 " pdb=" CA VAL A 50 " ideal model delta harmonic sigma weight residual 180.00 159.60 20.40 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.233: 113 0.233 - 0.462: 76 0.462 - 0.692: 35 0.692 - 0.922: 13 0.922 - 1.151: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA LYS A 32 " pdb=" N LYS A 32 " pdb=" C LYS A 32 " pdb=" CB LYS A 32 " both_signs ideal model delta sigma weight residual False 2.51 3.66 -1.15 2.00e-01 2.50e+01 3.31e+01 chirality pdb=" CA LEU A 128 " pdb=" N LEU A 128 " pdb=" C LEU A 128 " pdb=" CB LEU A 128 " both_signs ideal model delta sigma weight residual False 2.51 1.48 1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" CG LEU A 112 " pdb=" CB LEU A 112 " pdb=" CD1 LEU A 112 " pdb=" CD2 LEU A 112 " both_signs ideal model delta sigma weight residual False -2.59 -1.57 -1.02 2.00e-01 2.50e+01 2.59e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.134 2.00e-02 2.50e+03 6.91e-02 1.43e+02 pdb=" CG PHE A 119 " -0.109 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.104 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.043 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.045 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.086 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.022 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.046 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.038 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.102 2.00e-02 2.50e+03 6.56e-02 1.29e+02 pdb=" CG PHE A 164 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.045 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.142 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.043 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.040 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.026 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 98 " 0.063 9.50e-02 1.11e+02 7.48e-02 1.16e+02 pdb=" NE ARG A 98 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 98 " 0.059 2.00e-02 2.50e+03 pdb=" NH1 ARG A 98 " 0.077 2.00e-02 2.50e+03 pdb=" NH2 ARG A 98 " -0.123 2.00e-02 2.50e+03 pdb="HH11 ARG A 98 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A 98 " -0.100 2.00e-02 2.50e+03 pdb="HH21 ARG A 98 " -0.009 2.00e-02 2.50e+03 pdb="HH22 ARG A 98 " 0.108 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.34: 1176 2.34 - 2.91: 8301 2.91 - 3.47: 10440 3.47 - 4.04: 15158 4.04 - 4.60: 21573 Nonbonded interactions: 56648 Sorted by model distance: nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.777 2.100 nonbonded pdb=" OE2 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.793 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.836 2.450 nonbonded pdb=" H VAL A 44 " pdb=" O ILE A 52 " model vdw 1.837 2.450 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.841 2.100 ... (remaining 56643 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 3 O 551 7.97 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_6024882_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2610 r_free= 0.1931 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788184 | | target function (ml) not normalized (work): 232272.451099 | | target function (ml) not normalized (free): 11793.114391 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.58 1.00 2941 171 0.3031 0.2065 7.0541 4.9477| | 2: 3.57 - 2.84 1.00 2876 122 0.2448 0.1800 4.3516 4.3374| | 3: 2.84 - 2.48 1.00 2833 165 0.2337 0.1741 4.1244 4.1652| | 4: 2.47 - 2.25 1.00 2825 136 0.2350 0.1410 3.8311 3.8081| | 5: 2.25 - 2.09 1.00 2756 127 0.2495 0.1542 3.7955 3.8012| | 6: 2.09 - 1.97 1.00 2846 113 0.2576 0.1793 3.4607 3.5704| | 7: 1.97 - 1.87 1.00 2787 165 0.2477 0.1738 3.1167 3.1674| | 8: 1.87 - 1.79 1.00 2789 144 0.2492 0.1802 3.0487 3.1187| | 9: 1.79 - 1.72 1.00 2745 138 0.2434 0.1812 2.8938 2.908| | 10: 1.72 - 1.66 1.00 2789 158 0.2360 0.2042 2.7924 2.9151| | 11: 1.66 - 1.61 1.00 2740 147 0.2494 0.1849 2.7329 2.7266| | 12: 1.61 - 1.56 1.00 2787 146 0.2516 0.1794 2.6279 2.5434| | 13: 1.56 - 1.52 1.00 2745 130 0.2588 0.2049 2.5587 2.7548| | 14: 1.52 - 1.48 1.00 2803 134 0.2546 0.1858 2.5002 2.5217| | 15: 1.48 - 1.45 1.00 2738 128 0.2577 0.2173 2.4268 2.5063| | 16: 1.45 - 1.42 1.00 2756 161 0.2650 0.2271 2.3834 2.4523| | 17: 1.42 - 1.39 1.00 2785 139 0.2701 0.2102 2.3341 2.362| | 18: 1.39 - 1.36 1.00 2741 179 0.2727 0.2167 2.2911 2.321| | 19: 1.36 - 1.34 1.00 2807 134 0.2681 0.2047 2.2511 2.2149| | 20: 1.34 - 1.32 1.00 2696 147 0.2725 0.2300 2.2047 2.2533| | 21: 1.32 - 1.30 1.00 2785 112 0.2696 0.2308 2.1527 2.1539| | 22: 1.29 - 1.27 1.00 2704 152 0.2738 0.2491 2.1313 2.169| | 23: 1.27 - 1.26 1.00 2802 156 0.2805 0.2433 2.1187 2.1486| | 24: 1.26 - 1.24 1.00 2744 132 0.2800 0.2552 2.0695 2.1697| | 25: 1.24 - 1.22 1.00 2734 148 0.2868 0.2664 2.0511 2.125| | 26: 1.22 - 1.21 1.00 2727 135 0.2875 0.2540 2.0088 2.1315| | 27: 1.21 - 1.19 1.00 2814 148 0.2943 0.2553 2.0065 1.9815| | 28: 1.19 - 1.18 1.00 2671 147 0.2953 0.2639 1.9763 1.9624| | 29: 1.18 - 1.16 1.00 2800 134 0.2956 0.2658 1.968 2.0231| | 30: 1.16 - 1.15 1.00 2740 148 0.3084 0.2759 1.9265 1.9575| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.58 2941 171 0.87 18.87 0.76 0.23 1474.51| | 2: 3.57 - 2.84 2876 122 0.80 26.10 1.27 0.23 1474.51| | 3: 2.84 - 2.48 2833 165 0.74 31.91 1.24 0.23 1221.30| | 4: 2.47 - 2.25 2825 136 0.81 25.32 1.26 0.25 564.16| | 5: 2.25 - 2.09 2756 127 0.77 29.10 1.29 0.25 564.16| | 6: 2.09 - 1.97 2846 113 0.84 22.18 1.30 0.25 305.97| | 7: 1.97 - 1.87 2787 165 0.90 15.92 1.27 0.26 85.77| | 8: 1.87 - 1.79 2789 144 0.87 20.29 1.25 0.26 85.77| | 9: 1.79 - 1.72 2745 138 0.88 18.38 1.23 0.26 52.93| | 10: 1.72 - 1.66 2789 158 0.87 19.74 1.22 0.25 46.35| | 11: 1.66 - 1.61 2740 147 0.86 20.87 1.25 0.25 44.79| | 12: 1.61 - 1.56 2787 146 0.89 18.21 1.23 0.25 28.98| | 13: 1.56 - 1.52 2745 130 0.86 20.46 1.25 0.25 28.98| | 14: 1.52 - 1.48 2803 134 0.86 20.85 1.23 0.25 26.11| | 15: 1.48 - 1.45 2738 128 0.87 20.18 1.22 0.25 20.87| | 16: 1.45 - 1.42 2756 161 0.85 21.89 1.24 0.25 20.87| | 17: 1.42 - 1.39 2785 139 0.86 21.01 1.23 0.25 17.63| | 18: 1.39 - 1.36 2741 179 0.86 21.07 1.23 0.25 15.76| | 19: 1.36 - 1.34 2807 134 0.85 22.09 1.21 0.25 15.76| | 20: 1.34 - 1.32 2696 147 0.87 20.97 1.22 0.24 12.97| | 21: 1.32 - 1.30 2785 112 0.86 21.91 1.20 0.24 12.78| | 22: 1.29 - 1.27 2704 152 0.85 22.57 1.21 0.24 12.49| | 23: 1.27 - 1.26 2802 156 0.86 21.89 1.22 0.24 11.01| | 24: 1.26 - 1.24 2744 132 0.85 22.83 1.20 0.24 11.01| | 25: 1.24 - 1.22 2734 148 0.84 23.78 1.20 0.24 10.44| | 26: 1.22 - 1.21 2727 135 0.84 23.92 1.20 0.23 9.81| | 27: 1.21 - 1.19 2814 148 0.83 24.62 1.20 0.23 9.81| | 28: 1.19 - 1.18 2671 147 0.83 24.90 1.18 0.23 9.02| | 29: 1.18 - 1.16 2800 134 0.83 24.77 1.15 0.23 8.72| | 30: 1.16 - 1.15 2740 148 0.81 26.73 1.15 0.23 8.72| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.72 max = 1474.51 mean = 212.92| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.97 mean = 22.45| |phase err.(test): min = 0.00 max = 89.46 mean = 22.32| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.226 1557 Z= 5.599 Angle : 5.311 18.178 2118 Z= 3.853 Chirality : 0.388 1.151 243 Planarity : 0.032 0.111 284 Dihedral : 14.207 106.782 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.86 % Allowed : 3.11 % Favored : 95.03 % Cbeta Deviations : 31.89 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.48), residues: 224 helix: -2.67 (0.37), residues: 109 sheet: -0.75 (0.80), residues: 38 loop : -0.49 (0.64), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.058 0.016 ARG A 98 TYR 0.077 0.032 TYR A 141 PHE 0.127 0.044 PHE A 119 HIS 0.040 0.023 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2610 r_free= 0.1931 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788184 | | target function (ml) not normalized (work): 232272.451099 | | target function (ml) not normalized (free): 11793.114391 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2568 0.2611 0.1931 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2568 0.2611 0.1931 n_refl.: 87602 remove outliers: r(all,work,free)=0.1978 0.1982 0.1931 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2003 0.2008 0.1944 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1640 0.1634 0.1761 n_refl.: 87594 remove outliers: r(all,work,free)=0.1639 0.1633 0.1761 n_refl.: 87593 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3818 386.333 358.967 0.677 1.002 0.413 11.894-9.307 99.02 97 4 0.1757 613.671 594.432 0.930 1.003 0.379 9.237-7.194 100.00 213 7 0.2105 501.907 490.587 0.954 1.003 0.349 7.162-5.571 100.00 427 22 0.2159 376.653 364.589 0.932 1.003 0.340 5.546-4.326 100.00 867 58 0.1265 517.052 511.774 0.964 1.003 0.223 4.315-3.360 100.00 1859 96 0.1125 491.720 487.888 1.004 1.003 0.189 3.356-2.611 100.00 3867 181 0.1451 323.035 319.557 0.995 1.002 0.038 2.608-2.026 99.99 8198 413 0.1351 214.142 212.160 1.009 1.001 0.000 2.025-1.573 100.00 17313 902 0.1637 104.576 103.962 1.010 1.000 0.000 1.573-1.221 100.00 36679 1900 0.2069 46.373 45.059 1.005 0.997 0.000 1.221-1.150 99.97 13689 708 0.2597 29.218 26.984 0.972 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0472 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1633 r_free=0.1761 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A Total number of N/Q/H flips: 3 r_work=0.1642 r_free=0.1776 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.740448 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2034.726664 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1209 0.1470 0.0260 0.008 1.0 0.6 0.5 0.0 0 14.370 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.09 14.70 2.60 3.012 19.065 2034.727 0.017 12.43 15.42 2.99 3.373 19.674 2034.727 0.016 Individual atomic B min max mean iso aniso Overall: 8.73 118.89 21.25 2.90 0 1785 Protein: 8.73 118.89 18.07 2.90 0 1519 Water: 11.23 114.51 39.66 N/A 0 258 Other: 23.69 37.86 29.92 N/A 0 8 Chain A: 8.73 118.89 21.25 N/A 0 1785 Histogram: Values Number of atoms 8.73 - 19.74 1210 19.74 - 30.76 224 30.76 - 41.77 162 41.77 - 52.79 104 52.79 - 63.81 52 63.81 - 74.82 17 74.82 - 85.84 9 85.84 - 96.85 2 96.85 - 107.87 2 107.87 - 118.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1244 r_free=0.1542 r_work=0.1247 r_free=0.1546 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1247 r_free = 0.1546 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1247 r_free = 0.1545 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1247 r_free= 0.1545 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015440 | | target function (ls_wunit_k1) not normalized (work): 1286.134666 | | target function (ls_wunit_k1) not normalized (free): 114.082106 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1262 0.1247 0.1545 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1713 0.1712 0.1772 n_refl.: 87593 remove outliers: r(all,work,free)=0.1713 0.1712 0.1772 n_refl.: 87593 overall B=0.12 to atoms: r(all,work,free)=0.1734 0.1733 0.1787 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1259 0.1245 0.1536 n_refl.: 87593 remove outliers: r(all,work,free)=0.1258 0.1244 0.1536 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3610 297.789 277.554 0.631 1.001 0.380 11.894-9.307 99.02 97 4 0.1597 477.041 464.403 0.907 1.001 0.380 9.237-7.194 100.00 213 7 0.1825 390.161 384.569 0.945 1.002 0.340 7.162-5.571 100.00 427 22 0.1720 292.794 287.243 0.924 1.002 0.290 5.546-4.326 100.00 867 58 0.0912 401.934 399.842 0.949 1.002 0.209 4.315-3.360 100.00 1859 96 0.0769 382.242 380.987 0.994 1.002 0.190 3.356-2.611 100.00 3867 181 0.1019 251.113 250.403 0.997 1.002 0.048 2.608-2.026 99.99 8198 413 0.0981 166.465 165.851 1.010 1.002 0.000 2.025-1.573 100.00 17313 902 0.1217 81.293 81.504 1.015 1.002 0.000 1.573-1.221 100.00 36679 1900 0.1650 36.049 35.498 1.003 1.003 0.000 1.221-1.150 99.97 13689 708 0.2360 22.713 21.130 0.961 1.003 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0476 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1244 r_free=0.1536 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1244 r_free=0.1536 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1244 r_free=0.1536 | n_water=258 | time (s): 2.260 (total time: 2.260) Filter (dist) r_work=0.1259 r_free=0.1533 | n_water=251 | time (s): 27.450 (total time: 29.710) Filter (q & B) r_work=0.1262 r_free=0.1532 | n_water=248 | time (s): 3.780 (total time: 33.490) Compute maps r_work=0.1262 r_free=0.1532 | n_water=248 | time (s): 1.810 (total time: 35.300) Filter (map) r_work=0.1282 r_free=0.1542 | n_water=233 | time (s): 3.690 (total time: 38.990) Find peaks r_work=0.1282 r_free=0.1542 | n_water=233 | time (s): 0.690 (total time: 39.680) Add new water r_work=0.1441 r_free=0.1692 | n_water=456 | time (s): 3.680 (total time: 43.360) Refine new water occ: r_work=0.1339 r_free=0.1561 adp: r_work=0.1256 r_free=0.1500 occ: r_work=0.1269 r_free=0.1501 adp: r_work=0.1233 r_free=0.1481 occ: r_work=0.1237 r_free=0.1476 adp: r_work=0.1226 r_free=0.1474 ADP+occupancy (water only), MIN, final r_work=0.1226 r_free=0.1474 r_work=0.1226 r_free=0.1474 | n_water=456 | time (s): 103.890 (total time: 147.250) Filter (q & B) r_work=0.1232 r_free=0.1477 | n_water=433 | time (s): 3.860 (total time: 151.110) Filter (dist only) r_work=0.1232 r_free=0.1477 | n_water=433 | time (s): 40.360 (total time: 191.470) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.914798 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1487.128688 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1233 0.1515 0.0282 0.007 0.9 1.3 0.5 0.0 0 12.457 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.33 15.15 2.82 3.832 23.408 1487.129 0.015 12.09 15.00 2.91 4.310 23.177 1487.129 0.015 Individual atomic B min max mean iso aniso Overall: 8.73 114.01 23.33 2.62 200 1760 Protein: 8.73 114.01 17.79 2.63 0 1519 Water: 10.91 72.71 42.68 N/A 200 233 Other: 22.75 34.18 27.36 N/A 0 8 Chain A: 8.73 114.01 20.49 N/A 0 1760 Chain S: 17.70 70.98 48.31 N/A 200 0 Histogram: Values Number of atoms 8.73 - 19.26 1204 19.26 - 29.79 250 29.79 - 40.32 189 40.32 - 50.84 133 50.84 - 61.37 117 61.37 - 71.90 54 71.90 - 82.43 7 82.43 - 92.95 2 92.95 - 103.48 2 103.48 - 114.01 2 =========================== Idealize ADP of riding H ========================== r_work=0.1209 r_free=0.1501 r_work=0.1209 r_free=0.1500 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1209 r_free = 0.1500 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1210 r_free = 0.1495 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1210 r_free= 0.1495 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014149 | | target function (ls_wunit_k1) not normalized (work): 1178.528583 | | target function (ls_wunit_k1) not normalized (free): 106.006308 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1224 0.1210 0.1495 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1620 0.1615 0.1740 n_refl.: 87592 remove outliers: r(all,work,free)=0.1620 0.1615 0.1740 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1624 0.1620 0.1742 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1221 0.1208 0.1488 n_refl.: 87592 remove outliers: r(all,work,free)=0.1220 0.1206 0.1488 n_refl.: 87589 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3438 293.742 271.862 0.577 1.002 0.350 11.894-9.307 99.02 97 4 0.1572 477.041 473.996 0.913 1.002 0.337 9.237-7.194 100.00 213 7 0.1681 390.161 389.832 0.976 1.003 0.270 7.162-5.571 100.00 427 22 0.1521 292.794 289.331 0.944 1.003 0.260 5.546-4.326 100.00 867 58 0.0847 401.934 399.042 0.958 1.002 0.210 4.315-3.360 100.00 1859 96 0.0720 382.242 381.212 1.002 1.002 0.203 3.356-2.611 100.00 3867 181 0.0954 251.113 250.498 1.009 1.002 0.130 2.608-2.026 99.99 8198 413 0.0963 166.465 166.084 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1192 81.293 81.479 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1629 36.049 35.553 1.019 0.998 0.000 1.221-1.150 99.97 13689 708 0.2354 22.713 21.267 0.978 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0460 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1206 r_free=0.1488 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1206 r_free=0.1488 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1206 r_free=0.1488 | n_water=433 | time (s): 1.940 (total time: 1.940) Filter (dist) r_work=0.1206 r_free=0.1487 | n_water=431 | time (s): 39.350 (total time: 41.290) Filter (q & B) r_work=0.1206 r_free=0.1487 | n_water=431 | time (s): 1.140 (total time: 42.430) Compute maps r_work=0.1206 r_free=0.1487 | n_water=431 | time (s): 1.830 (total time: 44.260) Filter (map) r_work=0.1246 r_free=0.1488 | n_water=294 | time (s): 3.310 (total time: 47.570) Find peaks r_work=0.1246 r_free=0.1488 | n_water=294 | time (s): 0.720 (total time: 48.290) Add new water r_work=0.1371 r_free=0.1593 | n_water=481 | time (s): 2.780 (total time: 51.070) Refine new water occ: r_work=0.1273 r_free=0.1515 adp: r_work=0.1273 r_free=0.1517 occ: r_work=0.1251 r_free=0.1493 adp: r_work=0.1248 r_free=0.1493 occ: r_work=0.1236 r_free=0.1479 adp: r_work=0.1228 r_free=0.1476 ADP+occupancy (water only), MIN, final r_work=0.1228 r_free=0.1476 r_work=0.1228 r_free=0.1476 | n_water=481 | time (s): 250.640 (total time: 301.710) Filter (q & B) r_work=0.1232 r_free=0.1478 | n_water=447 | time (s): 3.580 (total time: 305.290) Filter (dist only) r_work=0.1232 r_free=0.1477 | n_water=446 | time (s): 38.320 (total time: 343.610) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.042633 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 54.568187 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1233 0.1438 0.0206 0.006 0.9 2.2 0.5 0.0 0 1.021 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.33 14.38 2.06 3.647 22.268 54.568 3.726 12.09 13.82 1.73 4.287 22.045 54.568 3.646 Individual atomic B min max mean iso aniso Overall: 9.25 109.04 21.78 2.36 215 1758 Protein: 9.25 109.04 17.23 2.36 0 1519 Water: 11.56 71.17 37.25 N/A 215 231 Other: 18.61 30.26 23.88 N/A 0 8 Chain A: 9.25 109.04 19.91 N/A 0 1758 Chain S: 16.52 61.26 37.10 N/A 215 0 Histogram: Values Number of atoms 9.25 - 19.23 1235 19.23 - 29.21 261 29.21 - 39.19 216 39.19 - 49.17 144 49.17 - 59.15 84 59.15 - 69.12 20 69.12 - 79.10 7 79.10 - 89.08 2 89.08 - 99.06 2 99.06 - 109.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1210 r_free=0.1382 r_work=0.1210 r_free=0.1383 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1210 r_free = 0.1383 target_work(ml) = 3.646 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1378 target_work(ml) = 3.643 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1204 r_free= 0.1378 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.642825 | | target function (ml) not normalized (work): 303421.849546 | | target function (ml) not normalized (free): 16021.930755 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1204 0.1378 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1548 0.1547 0.1596 n_refl.: 87589 remove outliers: r(all,work,free)=0.1548 0.1547 0.1596 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1547 0.1546 0.1596 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1198 0.1366 n_refl.: 87589 remove outliers: r(all,work,free)=0.1205 0.1196 0.1366 n_refl.: 87585 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.4160 288.357 262.892 0.488 0.999 0.330 11.894-9.307 99.02 97 4 0.2373 477.041 462.242 0.857 1.000 0.330 9.237-7.194 98.64 210 7 0.2310 382.732 383.291 0.960 1.001 0.200 7.162-5.571 100.00 427 22 0.2034 292.794 282.802 0.922 1.001 0.175 5.546-4.326 100.00 867 58 0.1081 401.934 397.250 0.959 1.001 0.170 4.315-3.360 100.00 1859 96 0.0918 382.242 379.552 1.003 1.002 0.170 3.356-2.611 100.00 3867 181 0.1149 251.113 249.322 1.008 1.002 0.072 2.608-2.026 99.99 8198 413 0.1048 166.465 165.524 1.020 1.002 0.000 2.025-1.573 100.00 17313 902 0.1014 81.293 81.465 1.034 1.002 0.000 1.573-1.221 100.00 36679 1900 0.1296 36.049 35.601 1.026 1.002 0.000 1.221-1.150 99.97 13689 708 0.2131 22.713 21.237 0.979 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0187 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1366 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1196 r_free=0.1366 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1366 | n_water=446 | time (s): 1.520 (total time: 1.520) Filter (dist) r_work=0.1196 r_free=0.1366 | n_water=446 | time (s): 34.220 (total time: 35.740) Filter (q & B) r_work=0.1196 r_free=0.1366 | n_water=446 | time (s): 1.310 (total time: 37.050) Compute maps r_work=0.1196 r_free=0.1366 | n_water=446 | time (s): 1.690 (total time: 38.740) Filter (map) r_work=0.1219 r_free=0.1372 | n_water=310 | time (s): 2.730 (total time: 41.470) Find peaks r_work=0.1219 r_free=0.1372 | n_water=310 | time (s): 0.440 (total time: 41.910) Add new water r_work=0.1290 r_free=0.1441 | n_water=476 | time (s): 2.850 (total time: 44.760) Refine new water occ: r_work=0.1213 r_free=0.1369 adp: r_work=0.1214 r_free=0.1370 occ: r_work=0.1198 r_free=0.1359 adp: r_work=0.1196 r_free=0.1357 occ: r_work=0.1187 r_free=0.1356 adp: r_work=0.1183 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1350 r_work=0.1183 r_free=0.1350 | n_water=476 | time (s): 160.830 (total time: 205.590) Filter (q & B) r_work=0.1190 r_free=0.1358 | n_water=440 | time (s): 2.920 (total time: 208.510) Filter (dist only) r_work=0.1196 r_free=0.1356 | n_water=438 | time (s): 34.930 (total time: 243.440) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.986343 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 50.190376 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1200 0.1372 0.0172 0.006 1.0 1.9 0.5 0.0 0 0.993 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 13.72 1.72 3.433 21.491 50.190 3.637 11.91 13.71 1.80 3.736 21.389 50.190 3.622 Individual atomic B min max mean iso aniso Overall: 9.20 104.43 21.27 2.19 209 1756 Protein: 9.20 104.43 17.01 2.20 0 1519 Water: 11.58 69.92 36.00 N/A 209 229 Other: 17.73 27.27 22.31 N/A 0 8 Chain A: 9.20 104.43 19.61 N/A 0 1756 Chain S: 16.38 56.79 35.18 N/A 209 0 Histogram: Values Number of atoms 9.20 - 18.72 1220 18.72 - 28.24 278 28.24 - 37.77 213 37.77 - 47.29 138 47.29 - 56.81 78 56.81 - 66.34 24 66.34 - 75.86 9 75.86 - 85.38 1 85.38 - 94.90 2 94.90 - 104.43 2 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1371 r_work=0.1192 r_free=0.1371 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1371 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1187 r_free = 0.1368 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87585 (all), 4.90 % free)------------| | | | r_work= 0.1187 r_free= 0.1368 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.620467 | | target function (ml) not normalized (work): 301545.071619 | | target function (ml) not normalized (free): 15935.249229 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1187 0.1368 n_refl.: 87585 re-set all scales: r(all,work,free)=0.1542 0.1541 0.1575 n_refl.: 87585 remove outliers: r(all,work,free)=0.1542 0.1541 0.1575 n_refl.: 87585 overall B=-0.01 to atoms: r(all,work,free)=0.1539 0.1539 0.1573 n_refl.: 87585 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1187 0.1369 n_refl.: 87585 remove outliers: r(all,work,free)=0.1193 0.1184 0.1369 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.4009 285.909 250.496 0.439 1.000 0.293 11.894-9.307 97.06 95 4 0.2384 474.180 460.327 0.842 1.002 0.273 9.237-7.194 97.73 208 7 0.2412 382.808 377.067 0.921 1.002 0.170 7.162-5.571 100.00 427 22 0.2167 292.794 281.460 0.902 1.002 0.170 5.546-4.326 100.00 867 58 0.1124 401.934 397.901 0.953 1.002 0.150 4.315-3.360 100.00 1859 96 0.0945 382.242 379.567 0.994 1.002 0.140 3.356-2.611 100.00 3867 181 0.1159 251.113 249.211 1.000 1.002 0.053 2.608-2.026 99.99 8198 413 0.1041 166.465 165.535 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.0973 81.293 81.531 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1241 36.049 35.670 1.022 0.998 0.000 1.221-1.150 99.97 13689 708 0.2119 22.713 21.339 0.979 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0393 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1184 r_free=0.1369 After: r_work=0.1184 r_free=0.1369 ================================== NQH flips ================================== r_work=0.1184 r_free=0.1369 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1184 r_free=0.1369 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1184 r_free=0.1369 | n_water=438 | time (s): 2.130 (total time: 2.130) Filter (dist) r_work=0.1184 r_free=0.1369 | n_water=438 | time (s): 34.430 (total time: 36.560) Filter (q & B) r_work=0.1184 r_free=0.1371 | n_water=437 | time (s): 2.540 (total time: 39.100) Compute maps r_work=0.1184 r_free=0.1371 | n_water=437 | time (s): 1.340 (total time: 40.440) Filter (map) r_work=0.1217 r_free=0.1377 | n_water=327 | time (s): 3.140 (total time: 43.580) Find peaks r_work=0.1217 r_free=0.1377 | n_water=327 | time (s): 0.600 (total time: 44.180) Add new water r_work=0.1273 r_free=0.1429 | n_water=491 | time (s): 2.500 (total time: 46.680) Refine new water occ: r_work=0.1200 r_free=0.1364 adp: r_work=0.1200 r_free=0.1367 occ: r_work=0.1188 r_free=0.1349 adp: r_work=0.1187 r_free=0.1351 occ: r_work=0.1179 r_free=0.1338 adp: r_work=0.1175 r_free=0.1338 ADP+occupancy (water only), MIN, final r_work=0.1175 r_free=0.1338 r_work=0.1175 r_free=0.1338 | n_water=491 | time (s): 132.630 (total time: 179.310) Filter (q & B) r_work=0.1182 r_free=0.1346 | n_water=450 | time (s): 2.910 (total time: 182.220) Filter (dist only) r_work=0.1182 r_free=0.1342 | n_water=447 | time (s): 37.530 (total time: 219.750) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.952741 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 40.944436 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1204 0.1378 0.0174 0.007 1.0 2.9 0.5 0.0 0 0.976 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.04 13.78 1.74 3.313 21.223 40.944 3.626 12.10 13.79 1.69 3.558 21.142 40.944 3.624 Individual atomic B min max mean iso aniso Overall: 9.22 100.55 21.09 2.03 222 1752 Protein: 9.22 100.55 16.80 2.04 0 1519 Water: 11.41 69.02 35.63 N/A 222 225 Other: 17.89 25.09 21.75 N/A 0 8 Chain A: 9.22 100.55 19.33 N/A 0 1752 Chain S: 16.16 57.34 34.98 N/A 222 0 Histogram: Values Number of atoms 9.22 - 18.35 1217 18.35 - 27.49 275 27.49 - 36.62 214 36.62 - 45.75 149 45.75 - 54.89 72 54.89 - 64.02 30 64.02 - 73.15 12 73.15 - 82.29 2 82.29 - 91.42 1 91.42 - 100.55 2 =========================== Idealize ADP of riding H ========================== r_work=0.1210 r_free=0.1379 r_work=0.1210 r_free=0.1379 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1210 r_free = 0.1379 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1206 r_free = 0.1376 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1206 r_free= 0.1376 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.622286 | | target function (ml) not normalized (work): 301674.807279 | | target function (ml) not normalized (free): 15932.865472 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2921 171 0.1423 0.1388 5.707 5.6205| | 2: 3.57 - 2.84 1.00 2888 124 0.1126 0.1397 5.1868 5.2335| | 3: 2.83 - 2.48 1.00 2820 163 0.1234 0.1379 4.9968 5.0304| | 4: 2.47 - 2.25 1.00 2825 136 0.1047 0.1192 4.7019 4.751| | 5: 2.25 - 2.09 1.00 2756 127 0.1003 0.1148 4.6389 4.7065| | 6: 2.09 - 1.97 1.00 2846 113 0.0996 0.1213 4.3567 4.4677| | 7: 1.97 - 1.87 1.00 2787 165 0.1013 0.1224 4.0872 4.1895| | 8: 1.87 - 1.79 1.00 2789 144 0.1036 0.1259 4.0038 4.0851| | 9: 1.79 - 1.72 1.00 2745 138 0.0967 0.1318 3.7217 3.8957| | 10: 1.72 - 1.66 1.00 2831 160 0.1013 0.1265 3.6407 3.7874| | 11: 1.66 - 1.61 1.00 2712 147 0.0972 0.1096 3.5742 3.6189| | 12: 1.61 - 1.56 1.00 2773 144 0.0918 0.1146 3.348 3.4712| | 13: 1.56 - 1.52 1.00 2745 130 0.0988 0.1077 3.3413 3.4414| | 14: 1.52 - 1.48 1.00 2803 134 0.0997 0.1077 3.2644 3.319| | 15: 1.48 - 1.45 1.00 2738 128 0.1018 0.1329 3.1686 3.3298| | 16: 1.45 - 1.42 1.00 2756 161 0.1082 0.1310 3.1534 3.2646| | 17: 1.42 - 1.39 1.00 2785 139 0.1126 0.1304 3.1155 3.2322| | 18: 1.39 - 1.36 1.00 2741 179 0.1157 0.1380 3.0845 3.2643| | 19: 1.36 - 1.34 1.00 2807 134 0.1221 0.1604 3.0923 3.2646| | 20: 1.34 - 1.32 1.00 2696 147 0.1317 0.1482 3.0853 3.1309| | 21: 1.32 - 1.30 1.00 2785 112 0.1416 0.1637 3.0853 3.1669| | 22: 1.29 - 1.27 1.00 2704 152 0.1478 0.1917 3.0831 3.2882| | 23: 1.27 - 1.26 1.00 2802 156 0.1578 0.1867 3.1005 3.2155| | 24: 1.26 - 1.24 1.00 2744 132 0.1625 0.1744 3.091 3.19| | 25: 1.24 - 1.22 1.00 2733 148 0.1788 0.2300 3.1057 3.2827| | 26: 1.22 - 1.21 1.00 2727 135 0.1867 0.1778 3.1208 3.1888| | 27: 1.21 - 1.19 1.00 2814 148 0.2021 0.2114 3.1398 3.1527| | 28: 1.19 - 1.18 1.00 2671 147 0.2155 0.2325 3.1386 3.1607| | 29: 1.18 - 1.16 1.00 2800 134 0.2219 0.2349 3.1249 3.2152| | 30: 1.16 - 1.15 1.00 2739 148 0.2379 0.2488 3.1129 3.1649| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2921 171 0.95 8.62 1.00 0.97 5948.68| | 2: 3.57 - 2.84 2888 124 0.92 12.95 1.01 0.97 5948.68| | 3: 2.83 - 2.48 2820 163 0.89 17.09 0.99 0.97 4998.58| | 4: 2.47 - 2.25 2825 136 0.91 14.35 1.00 0.98 2548.56| | 5: 2.25 - 2.09 2756 127 0.90 16.50 1.01 0.98 2548.56| | 6: 2.09 - 1.97 2846 113 0.92 13.65 1.02 0.97 1517.63| | 7: 1.97 - 1.87 2787 165 0.94 10.92 1.02 0.97 638.39| | 8: 1.87 - 1.79 2789 144 0.91 14.59 1.00 0.97 638.39| | 9: 1.79 - 1.72 2745 138 0.93 11.64 0.98 0.97 344.65| | 10: 1.72 - 1.66 2831 160 0.93 12.44 0.98 0.97 285.82| | 11: 1.66 - 1.61 2712 147 0.93 13.08 0.98 0.97 272.61| | 12: 1.61 - 1.56 2773 144 0.95 9.60 0.99 0.97 148.03| | 13: 1.56 - 1.52 2745 130 0.94 11.19 1.02 0.97 148.03| | 14: 1.52 - 1.48 2803 134 0.94 11.33 1.02 0.97 132.21| | 15: 1.48 - 1.45 2738 128 0.95 10.49 1.02 0.98 103.25| | 16: 1.45 - 1.42 2756 161 0.94 11.67 1.02 0.98 103.25| | 17: 1.42 - 1.39 2785 139 0.94 11.50 1.01 0.98 93.23| | 18: 1.39 - 1.36 2741 179 0.94 11.81 1.01 0.98 87.44| | 19: 1.36 - 1.34 2807 134 0.94 12.34 1.00 0.98 87.44| | 20: 1.34 - 1.32 2696 147 0.94 12.51 0.99 0.97 82.33| | 21: 1.32 - 1.30 2785 112 0.93 13.45 0.99 0.97 81.97| | 22: 1.29 - 1.27 2704 152 0.93 13.97 0.99 0.96 82.09| | 23: 1.27 - 1.26 2802 156 0.92 14.92 0.98 0.95 82.70| | 24: 1.26 - 1.24 2744 132 0.92 15.01 0.97 0.95 82.70| | 25: 1.24 - 1.22 2733 148 0.91 16.45 0.96 0.94 84.18| | 26: 1.22 - 1.21 2727 135 0.90 18.13 1.03 0.93 85.82| | 27: 1.21 - 1.19 2814 148 0.89 18.80 1.03 0.93 85.82| | 28: 1.19 - 1.18 2671 147 0.88 20.30 1.01 0.93 89.20| | 29: 1.18 - 1.16 2800 134 0.88 20.63 1.00 0.93 90.48| | 30: 1.16 - 1.15 2739 148 0.86 22.07 0.99 0.93 90.48| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 81.97 max = 5948.68 mean = 940.46| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.97 mean = 14.05| |phase err.(test): min = 0.00 max = 89.09 mean = 14.13| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1214 0.1206 0.1376 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1543 0.1543 0.1588 n_refl.: 87579 remove outliers: r(all,work,free)=0.1543 0.1543 0.1588 n_refl.: 87579 overall B=-0.02 to atoms: r(all,work,free)=0.1540 0.1539 0.1585 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1214 0.1206 0.1378 n_refl.: 87579 remove outliers: r(all,work,free)=0.1214 0.1205 0.1378 n_refl.: 87577 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.4131 285.909 252.572 0.436 0.999 0.297 11.894-9.307 95.10 93 4 0.2466 474.347 443.578 0.828 1.002 0.235 9.237-7.194 97.73 208 7 0.2520 382.808 376.292 0.911 1.002 0.177 7.162-5.571 100.00 427 22 0.2261 292.794 281.377 0.899 1.002 0.162 5.546-4.326 100.00 867 58 0.1193 401.934 397.457 0.954 1.002 0.138 4.315-3.360 100.00 1859 96 0.0982 382.242 379.541 0.995 1.002 0.123 3.356-2.611 100.00 3867 181 0.1196 251.113 249.248 1.001 1.002 0.048 2.608-2.026 99.99 8198 413 0.1056 166.465 165.558 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0992 81.293 81.572 1.029 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1230 36.049 35.693 1.025 0.997 0.000 1.221-1.150 99.97 13689 708 0.2118 22.713 21.354 0.983 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0546 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2610 0.1931 0.083 5.311 8.8 119.3 19.9 258 0.000 1_bss: 0.1633 0.1761 0.083 5.311 9.1 119.5 20.1 258 0.000 1_settarget: 0.1633 0.1761 0.083 5.311 9.1 119.5 20.1 258 0.000 1_nqh: 0.1642 0.1776 0.083 5.311 9.1 119.5 20.1 258 0.010 1_weight: 0.1642 0.1776 0.083 5.311 9.1 119.5 20.1 258 0.010 1_xyzrec: 0.1209 0.1470 0.008 0.979 9.1 119.5 20.1 258 0.128 1_adp: 0.1244 0.1542 0.008 0.979 8.7 118.9 21.2 258 0.128 1_regHadp: 0.1247 0.1546 0.008 0.979 8.7 118.9 21.2 258 0.128 1_occ: 0.1247 0.1545 0.008 0.979 8.7 118.9 21.2 258 0.128 2_bss: 0.1244 0.1536 0.008 0.979 8.8 119.0 21.4 258 0.128 2_settarget: 0.1244 0.1536 0.008 0.979 8.8 119.0 21.4 258 0.128 2_updatecdl: 0.1244 0.1536 0.008 0.992 8.8 119.0 21.4 258 0.128 2_nqh: 0.1244 0.1536 0.008 0.992 8.8 119.0 21.4 258 0.125 2_sol: 0.1232 0.1477 0.008 0.992 8.8 119.0 23.7 433 n/a 2_weight: 0.1232 0.1477 0.008 0.992 8.8 119.0 23.7 433 n/a 2_xyzrec: 0.1233 0.1515 0.007 0.875 8.8 119.0 23.7 433 n/a 2_adp: 0.1209 0.1501 0.007 0.875 8.7 114.0 23.3 433 n/a 2_regHadp: 0.1209 0.1500 0.007 0.875 8.7 114.0 23.3 433 n/a 2_occ: 0.1210 0.1495 0.007 0.875 8.7 114.0 23.3 433 n/a 3_bss: 0.1206 0.1488 0.007 0.875 8.8 114.0 23.4 433 n/a 3_settarget: 0.1206 0.1488 0.007 0.875 8.8 114.0 23.4 433 n/a 3_updatecdl: 0.1206 0.1488 0.007 0.876 8.8 114.0 23.4 433 n/a 3_nqh: 0.1206 0.1488 0.007 0.876 8.8 114.0 23.4 433 n/a 3_sol: 0.1232 0.1477 0.007 0.876 8.8 114.0 22.2 446 n/a 3_weight: 0.1232 0.1477 0.007 0.876 8.8 114.0 22.2 446 n/a 3_xyzrec: 0.1233 0.1438 0.006 0.919 8.8 114.0 22.2 446 n/a 3_adp: 0.1210 0.1382 0.006 0.919 9.3 109.0 21.8 446 n/a 3_regHadp: 0.1210 0.1383 0.006 0.919 9.3 109.0 21.8 446 n/a 3_occ: 0.1204 0.1378 0.006 0.919 9.3 109.0 21.8 446 n/a 4_bss: 0.1196 0.1366 0.006 0.919 9.2 109.0 21.8 446 n/a 4_settarget: 0.1196 0.1366 0.006 0.919 9.2 109.0 21.8 446 n/a 4_updatecdl: 0.1196 0.1366 0.006 0.918 9.2 109.0 21.8 446 n/a 4_nqh: 0.1196 0.1366 0.006 0.918 9.2 109.0 21.8 446 n/a 4_sol: 0.1196 0.1356 0.006 0.918 9.2 109.0 21.5 438 n/a 4_weight: 0.1196 0.1356 0.006 0.918 9.2 109.0 21.5 438 n/a 4_xyzrec: 0.1200 0.1372 0.006 0.953 9.2 109.0 21.5 438 n/a 4_adp: 0.1191 0.1371 0.006 0.953 9.2 104.4 21.3 438 n/a 4_regHadp: 0.1192 0.1371 0.006 0.953 9.2 104.4 21.3 438 n/a 4_occ: 0.1187 0.1368 0.006 0.953 9.2 104.4 21.3 438 n/a 5_bss: 0.1184 0.1369 0.006 0.953 9.2 104.4 21.3 438 n/a 5_settarget: 0.1184 0.1369 0.006 0.953 9.2 104.4 21.3 438 n/a 5_updatecdl: 0.1184 0.1369 0.006 0.953 9.2 104.4 21.3 438 n/a 5_setrh: 0.1184 0.1369 0.006 0.953 9.2 104.4 21.3 438 n/a 5_nqh: 0.1184 0.1369 0.006 0.953 9.2 104.4 21.3 438 n/a 5_sol: 0.1182 0.1342 0.006 0.953 9.2 104.4 21.2 447 n/a 5_weight: 0.1182 0.1342 0.006 0.953 9.2 104.4 21.2 447 n/a 5_xyzrec: 0.1204 0.1378 0.007 1.049 9.2 104.4 21.2 447 n/a 5_adp: 0.1210 0.1379 0.007 1.049 9.2 100.6 21.1 447 n/a 5_regHadp: 0.1210 0.1379 0.007 1.049 9.2 100.6 21.1 447 n/a 5_occ: 0.1206 0.1376 0.007 1.049 9.2 100.6 21.1 447 n/a end: 0.1205 0.1378 0.007 1.049 9.2 100.5 21.1 447 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6024882_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6024882_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.7900 Refinement macro-cycles (run) : 3393.4900 Write final files (write_after_run_outputs) : 75.1500 Total : 3473.4300 Total CPU time: 58.49 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:09:20 PST -0800 (1735452560.11 s) Start R-work = 0.1633, R-free = 0.1761 Final R-work = 0.1205, R-free = 0.1378 =============================================================================== Job complete usr+sys time: 3625.18 seconds wall clock time: 64 minutes 49.61 seconds (3889.61 seconds total)